Merge pull request #32 from genenetwork/heatmap_decompose_db_retrieval

Heatmap decompose db retrieval

1 files changed, 133 insertions, 0 deletions

diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
new file mode 100644
index 0000000..38de0e2
--- /dev/null
+++ b/tests/unit/db/test_datasets.py
@@ -0,0 +1,133 @@
+"""Tests for gn3/db/datasets.py"""
+
+from unittest import mock, TestCase
+from gn3.db.datasets import (
+    retrieve_dataset_name,
+    retrieve_riset_fields,
+    retrieve_geno_riset_fields,
+    retrieve_publish_riset_fields,
+    retrieve_probeset_riset_fields)
+
+class TestDatasetsDBFunctions(TestCase):
+    """Test cases for datasets functions."""
+
+    def test_retrieve_dataset_name(self):
+        """Test that the function is called correctly."""
+        for trait_type, thresh, trait_name, dataset_name, columns, table in [
+                ["ProbeSet", 9, "probesetTraitName", "probesetDatasetName",
+                 "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"],
+                ["Geno", 3, "genoTraitName", "genoDatasetName",
+                 "Id, Name, FullName, ShortName", "GenoFreeze"],
+                ["Publish", 6, "publishTraitName", "publishDatasetName",
+                 "Id, Name, FullName, ShortName", "PublishFreeze"],
+                ["Temp", 4, "tempTraitName", "tempTraitName",
+                 "Id, Name, FullName, ShortName", "TempFreeze"]]:
+            db_mock = mock.MagicMock()
+            with self.subTest(trait_type=trait_type):
+                with db_mock.cursor() as cursor:
+                    cursor.fetchone.return_value = {}
+                    self.assertEqual(
+                        retrieve_dataset_name(
+                            trait_type, thresh, trait_name, dataset_name, db_mock),
+                        {})
+                    cursor.execute.assert_called_once_with(
+                        "SELECT {cols} "
+                        "FROM {table} "
+                        "WHERE public > %(threshold)s AND "
+                        "(Name = %(name)s "
+                        "OR FullName = %(name)s "
+                        "OR ShortName = %(name)s)".format(
+                            table=table, cols=columns),
+                        {"threshold": thresh, "name": dataset_name})
+
+    def test_retrieve_probeset_riset_fields(self):
+        """
+        Test that the `riset` and `riset_id` fields are retrieved appropriately
+        for the 'ProbeSet' trait type.
+        """
+        for trait_name, expected in [
+                ["testProbeSetName", {}]]:
+            db_mock = mock.MagicMock()
+            with self.subTest(trait_name=trait_name, expected=expected):
+                with db_mock.cursor() as cursor:
+                    cursor.execute.return_value = ()
+                    self.assertEqual(
+                        retrieve_probeset_riset_fields(trait_name, db_mock),
+                        expected)
+                    cursor.execute.assert_called_once_with(
+                        (
+                            "SELECT InbredSet.Name, InbredSet.Id"
+                            " FROM InbredSet, ProbeSetFreeze, ProbeFreeze"
+                            " WHERE ProbeFreeze.InbredSetId = InbredSet.Id"
+                            " AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId"
+                            " AND ProbeSetFreeze.Name = %(name)s"),
+                        {"name": trait_name})
+
+    def test_retrieve_riset_fields(self):
+        """
+        Test that the riset fields are set up correctly for the different trait
+        types.
+        """
+        for trait_type, trait_name, dataset_info, expected in [
+                ["Publish", "pubTraitName01", {"dataset_name": "pubDBName01"},
+                 {"dataset_name": "pubDBName01", "riset": ""}],
+                ["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"},
+                 {"dataset_name": "prbDBName01", "riset": ""}],
+                ["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"},
+                 {"dataset_name": "genoDBName01", "riset": ""}],
+                ["Temp", "tempTraitName01", {}, {"riset": ""}],
+                ]:
+            db_mock = mock.MagicMock()
+            with self.subTest(
+                    trait_type=trait_type, trait_name=trait_name,
+                    dataset_info=dataset_info):
+                with db_mock.cursor() as cursor:
+                    cursor.execute.return_value = ("riset_name", 0)
+                    self.assertEqual(
+                        retrieve_riset_fields(
+                            trait_type, trait_name, dataset_info, db_mock),
+                        expected)
+
+    def test_retrieve_publish_riset_fields(self):
+        """
+        Test that the `riset` and `riset_id` fields are retrieved appropriately
+        for the 'Publish' trait type.
+        """
+        for trait_name, expected in [
+                ["testPublishName", {}]]:
+            db_mock = mock.MagicMock()
+            with self.subTest(trait_name=trait_name, expected=expected):
+                with db_mock.cursor() as cursor:
+                    cursor.execute.return_value = ()
+                    self.assertEqual(
+                        retrieve_publish_riset_fields(trait_name, db_mock),
+                        expected)
+                    cursor.execute.assert_called_once_with(
+                        (
+                            "SELECT InbredSet.Name, InbredSet.Id"
+                            " FROM InbredSet, PublishFreeze"
+                            " WHERE PublishFreeze.InbredSetId = InbredSet.Id"
+                            " AND PublishFreeze.Name = %(name)s"),
+                        {"name": trait_name})
+
+    def test_retrieve_geno_riset_fields(self):
+        """
+        Test that the `riset` and `riset_id` fields are retrieved appropriately
+        for the 'Geno' trait type.
+        """
+        for trait_name, expected in [
+                ["testGenoName", {}]]:
+            db_mock = mock.MagicMock()
+            with self.subTest(trait_name=trait_name, expected=expected):
+                with db_mock.cursor() as cursor:
+                    cursor.execute.return_value = ()
+                    self.assertEqual(
+                        retrieve_geno_riset_fields(trait_name, db_mock),
+                        expected)
+                    cursor.execute.assert_called_once_with(
+                        (
+                            "SELECT InbredSet.Name, InbredSet.Id"
+                            " FROM InbredSet, GenoFreeze"
+                            " WHERE GenoFreeze.InbredSetId = InbredSet.Id"
+                            " AND GenoFreeze.Name = %(name)s"),
+                        {"name": trait_name})